/*
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.3.3
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2008, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * For more info, check our website at http://www.gromacs.org
 * 
 * And Hey:
 * Groningen Machine for Chemical Simulation
 */
/* This file is completely threadsafe - keep it that way! */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "assert.h"
#include "maths.h"
#include "macros.h"
#include "copyrite.h"
#include "bondf.h"
#include "string2.h"
#include "smalloc.h"
#include "sysstuff.h"
#include "confio.h"
#include "physics.h"
#include "statutil.h"
#include "vec.h"
#include "random.h"
#include "3dview.h"
#include "txtdump.h"
#include "readinp.h"
#include "names.h"
#include "toppush.h"
#include "pdb2top.h"
#include "gpp_nextnb.h"
#include "gpp_atomtype.h"
#include "g_x2top.h"
#include "fflibutil.h"

static void rd_nm2type_file(const char *fn,int *nnm,t_nm2type **nmp)
{
  FILE      *fp;
  gmx_bool      bCont;
  char      libfilename[128];
  char      format[128],f1[128];
  char      buf[1024],elem[16],type[16],nbbuf[16],**newbuf;
  int       i,nb,nnnm,line=1;
  double    qq,mm,*blen;
  t_nm2type *nm2t=NULL;
  
  fp = fflib_open(fn);
  if (NULL == fp)
    gmx_fatal(FARGS,"Can not find %s in library directory",fn);
    
  nnnm = *nnm;
  nm2t = *nmp;
  do {
    /* Read a line from the file */
    bCont = (fgets2(buf,1023,fp) != NULL); 
    
    if (bCont) {
      /* Remove comment */
      strip_comment(buf);
      if (sscanf(buf,"%s%s%lf%lf%d",elem,type,&qq,&mm,&nb) == 5) {
	/* If we can read the first four, there probably is more */
	srenew(nm2t,nnnm+1);
	snew(nm2t[nnnm].blen,nb);
	if (nb > 0) {
	  snew(newbuf,nb);
	  strcpy(format,"%*s%*s%*s%*s%*s");
	  for(i=0; (i<nb); i++) {
	    /* Complicated format statement */
	    strcpy(f1,format);
	    strcat(f1,"%s%lf");
	    if (sscanf(buf,f1,nbbuf,&(nm2t[nnnm].blen[i])) != 2)
	      gmx_fatal(FARGS,"Error on line %d of %s",line,libfilename);
	    newbuf[i] = strdup(nbbuf);
	    strcat(format,"%*s%*s");
	  }
	}
	else
	  newbuf = NULL;
	nm2t[nnnm].elem   = strdup(elem);
	nm2t[nnnm].type   = strdup(type);
	nm2t[nnnm].q      = qq;
	nm2t[nnnm].m      = mm;
	nm2t[nnnm].nbonds = nb;
	nm2t[nnnm].bond   = newbuf;
	nnnm++;
      }
      line++;
    }
  } while(bCont);
  ffclose(fp);
  
  *nnm = nnnm;
  *nmp = nm2t;
}

t_nm2type *rd_nm2type(const char *ffdir,int *nnm)
{
  int  nff,f;
  char **ff;
  t_nm2type *nm;

  nff = fflib_search_file_end(ffdir,".n2t",FALSE,&ff);
  *nnm = 0;
  nm   = NULL;
  for(f=0; f<nff; f++) {
    rd_nm2type_file(ff[f],nnm,&nm);
    sfree(ff[f]);
  }
  sfree(ff);

  return nm;
}

void dump_nm2type(FILE *fp,int nnm,t_nm2type nm2t[])
{
  int i,j;
  
  fprintf(fp,"; nm2type database\n");
  for(i=0; (i<nnm); i++) {
    fprintf(fp,"%-8s %-8s %8.4f %8.4f %-4d",
	    nm2t[i].elem,nm2t[i].type,
	    nm2t[i].q,nm2t[i].m,nm2t[i].nbonds);
    for(j=0; (j<nm2t[i].nbonds); j++)
      fprintf(fp," %-5s %6.4f",nm2t[i].bond[j],nm2t[i].blen[j]);
    fprintf(fp,"\n");
  }
}

enum { ematchNone, ematchWild, ematchElem, ematchExact, ematchNR };

static int match_str(const char *atom,const char *template_string)
{
  if (!atom || !template_string)
    return ematchNone;
  else if (gmx_strcasecmp(atom,template_string) == 0) 
    return ematchExact;
  else if (atom[0] == template_string[0])
    return ematchElem;
  else if (strcmp(template_string,"*") == 0) 
    return ematchWild;
  else
    return ematchNone;
}

int nm2type(int nnm,t_nm2type nm2t[],t_symtab *tab,t_atoms *atoms,
	    gpp_atomtype_t atype,int *nbonds,t_params *bonds)
{
  int cur = 0;
#define prev (1-cur)
  int i,j,k,m,n,nresolved,nb,maxbond,ai,aj,best,im,nqual[2][ematchNR];
  int *bbb,*n_mask,*m_mask,**match,**quality;
  char *aname_i,*aname_m,*aname_n,*type;
  double qq,mm;
  t_param *param;
      
  snew(param,1);
  maxbond = 0;
  for(i=0; (i<atoms->nr); i++) 
    maxbond = max(maxbond,nbonds[i]);
  if (debug)
    fprintf(debug,"Max number of bonds per atom is %d\n",maxbond);
  snew(bbb,maxbond);
  snew(n_mask,maxbond);
  snew(m_mask,maxbond);
  snew(match,maxbond);
  for(i=0; (i<maxbond); i++)
    snew(match[i],maxbond);
    
  nresolved = 0;
  for(i=0; (i<atoms->nr); i++) {
    aname_i = *atoms->atomname[i];
    nb = 0;
    for(j=0; (j<bonds->nr); j++) {
      ai = bonds->param[j].AI;
      aj = bonds->param[j].AJ;
      if (ai == i)
	bbb[nb++] = aj;
      else if (aj == i)
	bbb[nb++] = ai;
    }
    if (nb != nbonds[i])
      gmx_fatal(FARGS,"Counting number of bonds nb = %d, nbonds[%d] = %d",
		nb,i,nbonds[i]);
    if(debug) {
      fprintf(debug,"%4s has bonds to",aname_i);
      for(j=0; (j<nb); j++)
	fprintf(debug," %4s",*atoms->atomname[bbb[j]]);
      fprintf(debug,"\n");
    }    
    best = -1;
    for(k=0; (k<ematchNR); k++) 
      nqual[prev][k] = 0;
    
    /* First check for names */  
    for(k=0; (k<nnm); k++) {
      if (nm2t[k].nbonds == nb) {
	im = match_str(*atoms->atomname[i],nm2t[k].elem);
	if (im > ematchWild) {
	  for(j=0; (j<ematchNR); j++) 
	    nqual[cur][j] = 0;

	  /* Fill a matrix with matching quality */
	  for(m=0; (m<nb); m++) {
	    aname_m = *atoms->atomname[bbb[m]];
	    for(n=0; (n<nb); n++) {
	      aname_n = nm2t[k].bond[n];
	      match[m][n] = match_str(aname_m,aname_n);
	    }
	  }
	  /* Now pick the best matches */
	  for(m=0; (m<nb); m++) {
	    n_mask[m] = 0;
	    m_mask[m] = 0;
	  }
	  for(j=ematchNR-1; (j>0); j--) {
	    for(m=0; (m<nb); m++) {
	      for(n=0; (n<nb); n++) {
		if ((n_mask[n] == 0) && 
		    (m_mask[m] == 0) &&
		    (match[m][n] == j)) {
		  n_mask[n] = 1;
		  m_mask[m] = 1;
		  nqual[cur][j]++;
		}
	      }
	    }
	  }
	  if ((nqual[cur][ematchExact]+
	       nqual[cur][ematchElem]+
	       nqual[cur][ematchWild]) == nb) {
	    if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
		
		((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
		 (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
		
		((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
		 (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
		 (nqual[cur][ematchWild] > nqual[prev][ematchWild]))) {
	      best = k;
	      cur  = prev;
	    }
	  }
	}
      }
    }
    if (best != -1) {
      int  atomnr=0;
      real alpha=0;
	
      qq   = nm2t[best].q;
      mm   = nm2t[best].m;
      type = nm2t[best].type;
      
      if ((k = get_atomtype_type(type,atype)) == NOTSET) {
	atoms->atom[i].qB = alpha;
	atoms->atom[i].m = atoms->atom[i].mB = mm;
	k = add_atomtype(atype,tab,&(atoms->atom[i]),type,param,
			 atoms->atom[i].type,0,0,0,atomnr,0,0);
      }
      atoms->atom[i].type  = k;
      atoms->atom[i].typeB = k;
      atoms->atom[i].q  = qq;
      atoms->atom[i].qB = qq;
      atoms->atom[i].m  = mm;
      atoms->atom[i].mB = mm;
      nresolved++;
    }
    else {
      fprintf(stderr,"Can not find forcefield for atom %s-%d with %d bonds\n",
	      *atoms->atomname[i],i+1,nb);
    }
  }
  sfree(bbb);
  sfree(n_mask);
  sfree(m_mask);
  sfree(param);
  
  return nresolved;
}
     
